Included EBSeq for downstream differential expression analysis

[rsem.git] / EBSeq / man / PoolMatrix.Rd

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+\name{PoolMatrix}
+\alias{PoolMatrix}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+Generate the expression matrix from the output of GetData
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+PoolMatrix(Data, reads, type)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{Data}{
+The output from GetData function.
+}
+  \item{reads}{
+The total number of reads in each lane. Could be obtained from the RSEM outputs. 
+}
+  \item{type}{
+If type="S", the outputs will be the a matrix which transcript names in row and sample names in column.
+If type="G", the first column will be the group information. 
+
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+\item{PoolM}{The matrix of nu values}
+\item{PoolValue}{The matrix of expression values}
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+GetData
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--   or do  help(data=index)  for the standard data sets.
+
+## The function is currently defined as
+function(Data,reads,type)
+{
+poolnames=names(Data)
+poolM=NULL
+for (po in 1:8)
+       poolM=cbind(poolM,Data[[po]][,1])
+rownames(poolM)=rownames(Data[[1]])
+colnames(poolM)=poolnames
+
+#poolValue=poolM*reads
+poolValue=poolM
+for (col in 1:8)
+       poolValue[,col]=poolM[,col]*reads[col]
+poolValue=round(poolValue)
+if (type=="G")
+       {
+               poolM=cbind(Data[[1]][,2],poolM)
+               poolValue=cbind(Data[[1]][,2],poolValue)
+               colnames(poolM)=c("Groups",poolnames)
+               colnames(poolValue)=c("Groups",poolnames)
+       }
+poolOutput=list(poolM=poolM,poolValue=poolValue)
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line